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The Department of Health, which is expected to deny the allegations, feared that excessive demand for Viagra could cost the health service more than £1bn a year.
The drug was licensed for use in the European Union in September.
In January, the government issued further guidance to doctors, restricting the prescription of Viagra to men with specific medical conditions.
Consultation on this advice ended on 25 March and the government is still considering the results.
The British Medical Association has advised doctors that they have a contractual obligation to prescribe the drug to anyone with a clinical need.
It says the government's restrictions, which it calls "irrational and misguided", mean only 15% of patients with a clinical need will get the drug.
However, NHS managers, worried about their budgets, support it.
Judicial review
Pfizer's court action, which is due to begin next Monday or Tuesday, relates solely to last year's guidance.
It is seeking a judicial review of the guidance, saying the government acted illegally by not giving a good reason for its decision.
"They did not react quickly after issuing the advice and we have to protect our business interests," said a spokesman for Pfizer. It is a point of principle."
Pfizer says the government has received 850 replies to its consultation on Viagra.
About 250 have been copied to the company.
"They are more or less unanimous that the proposals are unfair and discriminatory," said the spokesman.
However, he added that, if the government decided to go ahead with its plans to restrict Viagra and legislated for them, it would not be able to take legal action - as it has over last year's guidance.
Difficult position
But he said the proposals would put doctors in a difficult position.
"They will not want to go against their employer, but it is hard to sit opposite a patient with an erectile dysfunction who has had the courage to speak to someone about it."
He added that the media hype had made people realise that impotence was a medical condition, that it could be treated and that they were not alone.
"After being turned away by the majority of doctors following the government's advice many men will never go back.
"That means doctors will miss the opportunity to diagnose the underlying cause of their impotence and it could be left until it is much more serious," he stated.
Background Briefings
Medical notes
NHS bosses: Restrict Viagra
(26 Mar 99 | Viagra)
'Give impotent men Viagra'
(25 Mar 99 | Viagra)
Pressure mounts for Viagra U-turn
(24 Mar 99 | Viagra)
Viagra patients could sue, says doctor
(25 Jan 99 | Viagra)
Viagra impotence warning
(28 Jan 99 | Viagra)
Doctors: why we oppose Viagra rationing
(21 Jan 99 | Viagra)
Viagra rival set for licence
(04 Jan 99 | Viagra)
GPs issue Viagra warning
(18 Dec 98 | Viagra)
Channel Island firms bypass Viagra ban
(15 Dec 98 | Viagra)
Pfizer
Department of Health
British Medical Association
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